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core::pack::dunbrack::SingleLigandRotamerLibrary Class Reference

A fixed library of conformations for some residue type (doesn't have to be a ligand). More...

#include <SingleLigandRotamerLibrary.hh>

Inheritance diagram for core::pack::dunbrack::SingleLigandRotamerLibrary:
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Public Member Functions

 SingleLigandRotamerLibrary ()
 
virtual ~SingleLigandRotamerLibrary ()
 
 SingleLigandRotamerLibrary (utility::vector1< conformation::ResidueOP > &rotamers_in, Real ref_E_in)
 explicit constructor More...
 
virtual void init_from_file (std::string const &filename, chemical::ResidueTypeCOP restype)
 Reads conformers from PDB-format file (must be separated by TER records!) More...
 
virtual Real rotamer_energy_deriv (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const
 Adheres to the contract from SingleLigandRotamerLibrary. More...
 
virtual Real rotamer_energy (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const
 Adheres to the contract from SingleLigandRotamerLibrary. More...
 
virtual Real best_rotamer_energy (conformation::Residue const &rsd, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const
 
virtual void assign_random_rotamer_with_bias (conformation::Residue const &, RotamerLibraryScratchSpace &, numeric::random::RandomGenerator &, ChiVector &, bool) const
 Pick a rotamer for the input residue according to the rotamer probability distribution and assign chi angles to the input rsd. If perturb_from_rotamer_center is true, then push the rotamer off from the center; for chi angles with a normal distribution, the perturbation is taken from a Gaussian random number with a standard deviation matching the chi angle's standard deviation. For chi angles that are not normally distributed, the behavior is open to the derived classe's interpretation. More...
 
virtual void fill_rotamer_vector (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, graph::GraphCOP, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, RotamerVector &rotamers) const
 Adheres to the contract from SingleLigandRotamerLibrary. More...
 
virtual void write_to_file (utility::io::ozstream &out) const
 Adheres to the contract from SingleLigandRotamerLibrary. More...
 
Real get_reference_energy () const
 
void set_reference_energy (Real ref_E_in)
 
void set_rotamers (utility::vector1< conformation::ResidueOP > &rotamers_in)
 
utility::vector1
< conformation::ResidueOP >
const & 
get_rotamers () const
 
- Public Member Functions inherited from core::pack::dunbrack::SingleResidueRotamerLibrary
virtual ~SingleResidueRotamerLibrary ()
 

Private Member Functions

void fill_missing_atoms (utility::vector1< bool > missing, conformation::ResidueOP rsd, utility::vector1< bool > &missed) const
 Fills in missing hydrogens/virtual atoms from library load. More...
 

Private Attributes

utility::vector1
< conformation::ResidueOP
rotamers_
 
Real ref_energy_
 

Detailed Description

A fixed library of conformations for some residue type (doesn't have to be a ligand).

Reads residue conformations in PDB format separated by mandatory TER records. "Included" from a residue .params file with the PDB_ROTAMERS keyword.

Constructor & Destructor Documentation

core::pack::dunbrack::SingleLigandRotamerLibrary::SingleLigandRotamerLibrary ( )
core::pack::dunbrack::SingleLigandRotamerLibrary::~SingleLigandRotamerLibrary ( )
virtual
core::pack::dunbrack::SingleLigandRotamerLibrary::SingleLigandRotamerLibrary ( utility::vector1< conformation::ResidueOP > &  rotamers_in,
Real  ref_E_in 
)

explicit constructor

Member Function Documentation

virtual void core::pack::dunbrack::SingleLigandRotamerLibrary::assign_random_rotamer_with_bias ( conformation::Residue const &  rsd,
RotamerLibraryScratchSpace scratch,
numeric::random::RandomGenerator &  RG,
ChiVector new_chi_angles,
bool  perturb_from_rotamer_center 
) const
inlinevirtual

Pick a rotamer for the input residue according to the rotamer probability distribution and assign chi angles to the input rsd. If perturb_from_rotamer_center is true, then push the rotamer off from the center; for chi angles with a normal distribution, the perturbation is taken from a Gaussian random number with a standard deviation matching the chi angle's standard deviation. For chi angles that are not normally distributed, the behavior is open to the derived classe's interpretation.

Implements core::pack::dunbrack::SingleResidueRotamerLibrary.

Real core::pack::dunbrack::SingleLigandRotamerLibrary::best_rotamer_energy ( conformation::Residue const &  rsd,
bool  curr_rotamer_only,
RotamerLibraryScratchSpace scratch 
) const
virtual

Not currently implemented – returns 0. For most things, it's actually quite hard to correctly rank the conformers by energy. Thus, I've chosen not to introduce noise by attempting to rank them and doing it badly.

Implements core::pack::dunbrack::SingleResidueRotamerLibrary.

References ref_energy_.

void core::pack::dunbrack::SingleLigandRotamerLibrary::fill_missing_atoms ( utility::vector1< bool missing,
conformation::ResidueOP  rsd,
utility::vector1< bool > &  missed 
) const
private

Fills in missing hydrogens/virtual atoms from library load.

"missing" is the vector for atoms missing for the current "rsd"

References core::pack::dunbrack::TR().

Referenced by init_from_file().

void core::pack::dunbrack::SingleLigandRotamerLibrary::fill_rotamer_vector ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scorefxn,
pack::task::PackerTask const &  task,
graph::GraphCOP  ,
chemical::ResidueTypeCOP  concrete_residue,
conformation::Residue const &  existing_residue,
utility::vector1< utility::vector1< Real > > const &  extra_chi_steps,
bool  buried,
RotamerVector rotamers 
) const
virtual
Real core::pack::dunbrack::SingleLigandRotamerLibrary::get_reference_energy ( ) const
inline

References ref_energy_.

utility::vector1< conformation::ResidueOP > const& core::pack::dunbrack::SingleLigandRotamerLibrary::get_rotamers ( ) const
inline

References rotamers_.

void core::pack::dunbrack::SingleLigandRotamerLibrary::init_from_file ( std::string const &  filename,
chemical::ResidueTypeCOP  restype 
)
virtual

Reads conformers from PDB-format file (must be separated by TER records!)

Reads conformers from PDB-format file. Chain ID, residue name and number, etc are all ignored – must have TER records.

References core::conformation::ResidueFactory::create_residue(), fill_missing_atoms(), ref_energy_, rotamers_, core::conformation::set_chi_according_to_coordinates(), and core::pack::dunbrack::TR().

Real core::pack::dunbrack::SingleLigandRotamerLibrary::rotamer_energy ( conformation::Residue const &  rsd,
RotamerLibraryScratchSpace scratch 
) const
virtual

Adheres to the contract from SingleLigandRotamerLibrary.

Not currently implemented – returns 0. For most things, it's actually quite hard to correctly rank the conformers by energy. Thus, I've chosen not to introduce noise by attempting to rank them and doing it badly.

Implements core::pack::dunbrack::SingleResidueRotamerLibrary.

References ref_energy_.

Referenced by rotamer_energy_deriv().

Real core::pack::dunbrack::SingleLigandRotamerLibrary::rotamer_energy_deriv ( conformation::Residue const &  rsd,
RotamerLibraryScratchSpace scratch 
) const
virtual
void core::pack::dunbrack::SingleLigandRotamerLibrary::set_reference_energy ( Real  ref_E_in)
inline

References ref_energy_.

void core::pack::dunbrack::SingleLigandRotamerLibrary::set_rotamers ( utility::vector1< conformation::ResidueOP > &  rotamers_in)
inline

References rotamers_.

void core::pack::dunbrack::SingleLigandRotamerLibrary::write_to_file ( utility::io::ozstream &  out) const
virtual

Adheres to the contract from SingleLigandRotamerLibrary.

Not implemented – will cause program termination. Is this only used by coarse representations?

Implements core::pack::dunbrack::SingleResidueRotamerLibrary.

Member Data Documentation

Real core::pack::dunbrack::SingleLigandRotamerLibrary::ref_energy_
private
utility::vector1< conformation::ResidueOP > core::pack::dunbrack::SingleLigandRotamerLibrary::rotamers_
private

The documentation for this class was generated from the following files: